Re: [gmx-users] rvdw and rcoulomb
On 3/13/18 7:23 AM, Ahmed Mashaly wrote: Dear Justin, What do you mean by incorrect? I understand it is higher than it should be (0.8 - 1 nm), it will consume more time, but won't give wrong results, am I correct? With PME, the value of rcoulomb becomes somewhat irrelevant, but in general, one should *not* deviate from prescribed force field cutoff values. Force fields are parametrized under a certain set of assumptions. If you then deviate from those assumptions, you potentially imbalance forces. The simulation will happily run and potentially produce incorrect results. Find the proper values in primary literature (something everyone should do before even deciding on a force field) and use those values. GROMACS will tune rcoulomb slightly for PME performance reasons, and this is fine, but don't go messing with the stock values haphazardly. -Justin Kind Regards, Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, March 13, 2018 12:18 PM Subject: Re: [gmx-users] rvdw and rcoulomb On 3/13/18 5:17 AM, Ahmed Mashaly wrote: Thanks guys It is AMBER ff Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results? You shouldn't switch physical models mid-simulation. Start over using the correct value (1.2 nm is incorrect for AMBER, anyway). -Justin On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll wrote: Note that rcoulomb, unlike rvdw, when using a PME long-range electrostatics, is tunable (together with the PME grid spacing). -- Szilárd On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: On 3/11/18 7:33 PM, Ahmed Mashaly wrote: Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed These values are a function of the force field and are not freely tunable. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rvdw and rcoulomb
Dear Justin, What do you mean by incorrect? I understand it is higher than it should be (0.8 - 1 nm), it will consume more time, but won't give wrong results, am I correct? Kind Regards, Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, March 13, 2018 12:18 PM Subject: Re: [gmx-users] rvdw and rcoulomb On 3/13/18 5:17 AM, Ahmed Mashaly wrote: > Thanks guys > > It is AMBER ff > Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 > for continuation with no effect on the results? And if I do the other > restarts starting from 1 or it will give different results? You shouldn't switch physical models mid-simulation. Start over using the correct value (1.2 nm is incorrect for AMBER, anyway). -Justin > On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll >> wrote: >> Note that rcoulomb, unlike rvdw, when using a PME long-range >> electrostatics, is tunable (together with the PME grid spacing). >> -- >> Szilárd >> >> >> On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: >>> >>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote: >>>> Dear users, >>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind >>>> Regards,Ahmed >>>> >>> These values are a function of the force field and are not freely tunable. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >>> mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rvdw and rcoulomb
On 3/13/18 5:17 AM, Ahmed Mashaly wrote: Thanks guys It is AMBER ff Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results? You shouldn't switch physical models mid-simulation. Start over using the correct value (1.2 nm is incorrect for AMBER, anyway). -Justin On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll wrote: Note that rcoulomb, unlike rvdw, when using a PME long-range electrostatics, is tunable (together with the PME grid spacing). -- Szilárd On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: On 3/11/18 7:33 PM, Ahmed Mashaly wrote: Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed These values are a function of the force field and are not freely tunable. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rvdw and rcoulomb
Thanks guys It is AMBER ff Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results? On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll > wrote: >Note that rcoulomb, unlike rvdw, when using a PME long-range >electrostatics, is tunable (together with the PME grid spacing). >-- >Szilárd > > >On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: >> >> >> On 3/11/18 7:33 PM, Ahmed Mashaly wrote: >>> >>> Dear users, >>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind >>> Regards,Ahmed >>> >> These values are a function of the force field and are not freely tunable. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> == >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rvdw and rcoulomb
Note that rcoulomb, unlike rvdw, when using a PME long-range electrostatics, is tunable (together with the PME grid spacing). -- Szilárd On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: > > > On 3/11/18 7:33 PM, Ahmed Mashaly wrote: >> >> Dear users, >> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind >> Regards,Ahmed >> > These values are a function of the force field and are not freely tunable. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] rvdw and rcoulomb
On 3/11/18 7:33 PM, Ahmed Mashaly wrote: Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed These values are a function of the force field and are not freely tunable. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] rvdw and rcoulomb
Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.